Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 1L0N


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLN*     3.2    11.1    -      -       -      +
     33A  PRO*     1.3    84.1    -      -       -      +
     35A  CYS*     1.3    77.4    +      -       -      +
    100A  LYS*     5.2     0.9    -      -       +      -
    101A  ALA      3.5    17.3    -      -       -      +
    102A  LEU*     4.5     5.8    -      -       +      +
    103A  SER*     3.6     2.7    +      -       -      +
    201A  GLY*     3.8     0.3    -      -       -      -
    202A  GLY      3.7     5.2    +      -       -      -
    372A  THR*     3.6    10.3    -      -       -      +
    366B  ALA      5.4     0.2    -      -       -      +
    369B  LEU*     3.6    30.1    +      -       -      +
    370B  MET*     3.5    25.0    +      -       +      +
    373B  GLU*     3.3    28.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  THR*     1.3    80.7    -      -       -      +
     36A  THR*     1.3    68.8    +      -       -      +
     37A  VAL*     4.2    18.4    -      -       -      -
    100A  LYS*     3.7     1.4    -      -       -      +
    101A  ALA*     2.9    47.9    +      -       -      -
    102A  LEU      4.0    11.2    -      -       -      -
    103A  SER*     4.0     5.4    -      -       -      +
    106A  LEU*     4.6     5.6    -      -       -      -
    109A  ALA*     6.1     0.2    -      -       -      -
    200A  ALA      3.2    15.5    -      -       -      +
    201A  GLY*     4.3     0.7    -      -       -      -
    203A  LEU*     3.6    29.4    -      -       +      -
    372A  THR*     3.6     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  CYS*     1.3    79.7    +      -       -      +
     37A  VAL*     1.3    63.2    +      -       -      +
     40A  TRP*     5.6     0.4    -      -       +      -
     98A  TYR*     4.3    19.5    -      -       +      -
     99A  ILE      3.4    11.0    -      -       -      +
    100A  LYS*     4.1     4.7    +      -       -      -
    199A  ALA*     3.1     5.1    -      -       -      -
    200A  ALA      3.1    26.3    +      -       -      -
    372A  THR*     2.7    35.7    +      -       -      -
    373A  THR*     2.8    27.6    +      -       +      +
    376A  CYS*     3.2    20.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  CYS*     4.2    10.3    -      -       -      -
     36A  THR*     1.3    75.7    -      -       -      +
     38A  GLY*     1.3    58.2    +      -       -      +
     98A  TYR*     3.2     4.3    -      -       -      +
     99A  ILE*     2.6    42.5    +      -       +      +
    101A  ALA*     5.7     0.4    -      -       +      +
    106A  LEU*     3.8    25.6    -      -       +      -
    109A  ALA*     3.8    25.6    -      -       +      -
    110A  VAL*     4.0    16.8    -      -       +      -
    113A  LEU*     3.5    10.0    -      -       +      +
    197A  LEU*     4.3    10.5    -      -       +      -
    198A  ALA      3.4     8.7    -      -       -      +
    199A  ALA*     3.9    13.0    -      -       +      -
    208A  LEU*     4.5     1.6    -      -       +      -
    376A  CYS*     4.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  VAL*     1.3    78.7    -      -       -      +
     39A  VAL*     1.3    61.4    +      -       -      -
     40A  TRP*     3.5    17.0    -      -       -      -
     97A  TYR      3.2    12.3    -      -       -      -
     98A  TYR*     3.8     1.1    -      -       -      -
    113A  LEU*     3.6     4.5    -      -       -      -
    196A  VAL      3.6     0.2    -      -       -      +
    197A  LEU*     3.4     5.7    -      -       -      +
    198A  ALA*     2.7    40.3    +      -       -      +
    376A  CYS*     4.0     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLY*     1.3    76.0    -      -       -      +
     40A  TRP*     1.3    63.1    +      -       -      +
     41A  ILE*     3.7    27.2    +      -       +      +
     95A  THR      4.0     0.2    -      -       -      +
     96A  ALA*     3.4     4.3    -      -       -      -
     97A  TYR*     2.9    34.0    +      -       +      +
    113A  LEU*     3.8    25.1    -      -       +      +
    117A  VAL*     4.1     7.4    -      -       +      -
    195A  MET*     3.8    25.1    -      -       +      -
    196A  VAL      3.5     5.6    -      -       -      +
    197A  LEU*     4.2     6.7    -      -       +      -
    216A  PHE*     4.1    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  THR*     5.6     0.4    -      -       +      -
     38A  GLY*     3.5    29.2    -      -       -      -
     39A  VAL*     1.3    76.6    -      -       -      +
     41A  ILE*     1.3    59.1    +      -       -      +
     89A  TYR*     2.9    22.7    +      +       -      -
     94A  HIS*     5.3     5.2    -      -       +      -
     95A  THR      3.7     4.9    -      -       -      -
     96A  ALA*     3.5    20.7    -      -       +      +
     97A  TYR      4.8     0.7    -      -       -      -
     98A  TYR*     3.9    26.7    -      +       +      -
    194A  ARG      3.8     0.5    -      -       -      +
    195A  MET*     3.1     4.9    -      -       -      +
    196A  VAL*     2.8    34.0    +      -       +      +
    198A  ALA*     4.3     2.5    -      -       +      -
    373A  THR      5.5     0.2    -      -       -      -
    376A  CYS*     3.8    17.9    -      -       +      -
    377A  GLU*     3.4    43.3    +      -       +      +
    380A  GLY*     3.9    24.5    -      -       -      +
    381A  ARG*     3.9    21.3    -      -       +      +
    384A  LEU*     3.8    18.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  VAL*     3.7    13.9    -      -       +      +
     40A  TRP*     1.3    79.3    -      -       -      +
     42A  ASP*     1.3    57.5    +      -       -      +
     43A  ALA*     2.7    33.5    +      -       +      +
     94A  HIS*     3.8     4.2    -      -       -      -
     95A  THR*     2.9    34.6    +      -       -      +
     97A  TYR*     4.2     9.9    -      -       +      -
    117A  VAL*     3.8    15.3    -      -       +      -
    189A  HIS      4.1    15.3    -      -       -      +
    190A  TYR*     3.5    43.5    -      -       +      +
    194A  ARG      3.3     8.5    -      -       -      +
    195A  MET*     3.8    10.3    -      -       +      -
    384A  LEU*     3.7     7.1    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il